Re: [AMBER] Make the two ligands independent in one simulation

From: Gustavo Seabra <gustavo.seabra.gmail.com> Date: Mon, 26 Apr 2021 14:51:29 -0400

--
Gustavo Seabra.
On Fri, Apr 23, 2021 at 10:47 PM 李明玉 <santaclaus.sjtu.edu.cn> wrote:
> Hi, Kress!
>
> Not really.
>
> Usually, small molecules tend to aggregate together to form a ball-like
> structure, and I want to prevent it in my simulation!
>
> One method is to applied repulsive forces between Virtual Interaction
> Sites (VIS) which are placed evenly all over the molecule.
> The repulsive force is formulated through the reassignment of the
> Lennard-Jones’ parameters.
>
> I am thinking of another possibility. Like the idea of a parallel
> universe, where I can put the ligands together in a single system ,
> however, they have no non-bond interactions, so that they would not
> aggregate together.
>
> I don't know if there are some "masks" to specifically disable the
> non-bond interaction only between the ligands without the impact on the
> interactions between the ligands and the protein.
>
> Thanks for your reply!
> Pineapple
>
> 发件人: "James Kress" <jimkress_58.kressworks.org>
> 收件人: "amber" <amber.ambermd.org>
> 发送时间: 星期六, 2021年 4 月 24日 上午 3:00:52
> 主题: Re: [AMBER] Make the two ligands independent in one simulation
>
> So, are you trying to modify the laws of Physics to prevent the simulation
> from providing physically accurate results?
>
> James Kress Ph.D., President
> The KressWorks(r) Institute
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
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> -----Original Message-----
> From: 李明玉 <santaclaus.sjtu.edu.cn>
> Sent: Friday, April 23, 2021 10:19 AM
> To: amber <amber.ambermd.org>
> Subject: [AMBER] Make the two ligands independent in one simulation
>
> Hi, Amber users
>
> Thanks for your attention!
>
> I would like to study two ligands binding behavior in one protein system
> simultaneously in a single MD trajectory.
>
> However, the ligands prefer to aggregate together due to the polarity.
>
> I am wondering is there any possible way to make those two ligands
> independent in a single MD trajectory.
> In other words, there is no non-bond energy between the two ligands, so
> that
> they can move independently though they are in one protein system!
>
> Many thanks
> Pineapple
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